SALON - Sequence ALignment ONtology
SALON.owl was developed using Protégé 5.5.0 (beta 5 SNAPSHOT).
You can directly load the ontology in Protégé using the provided URI:
Note: Unlike Virtuoso, Stardog supports SWRL rules (which this ontology makes use of). Therefore, this tool requires a running Stardog server instance to unlock all features, albeit Virtuoso or any other triple store can be used. You can deploy Stardog on Docker with:
$ docker run -it -v ~/your/license/folder/:/var/opt/stardog -p 5820:5820 stardog/stardog
To download and install the SALON companion client just clone the Git repository hosted in GitHub:
$ git clone git@github.com:benhid/SALON.git
$ cd salon
$ python setup.py install
Then, run
$ saloncli --help
Setup environmental variables as follows (using your own connection settings):
$ export STARDOG_ENDPOINT=http://localhost:5820
$ export STARDOG_USERNAME=admin
$ export STARDOG_PASSWORD=admin
$ export STARDOG_DATABASE=salon
Alternatively, create a dotenv file in the current directory and append the former variables.
Creates database in RDF repository
$ saloncli init -i SALON.owl
Transform sequence alignment from MACSIM/XML to Turtle
$ saloncli parse -i examples/BB11001.xml -o examples/BB11001.ttl
Populates RDF repository
$ saloncli load -i examples/BB11001.ttl
Enriches protein sequence given its URI
$ saloncli enrich -x https://w3id.org/salon#BB11001_1aab_
Generates UniprotKB FASTA header/description line for protein sequence given its URI
$ saloncli header -x https://w3id.org/salon#BB11001_1aab_
Documentation was generated with pyLODE 2.8.3:
$ make docs
— ⭐️ —
Designed & built by Khaos Research (University of Málaga).